Multiple sequence alignment - TraesCS2D01G259800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2D01G259800 chr2D 100.000 2978 0 0 3070 6047 316124499 316121522 0.000000e+00 5500.0
1 TraesCS2D01G259800 chr2D 100.000 2780 0 0 1 2780 316127568 316124789 0.000000e+00 5134.0
2 TraesCS2D01G259800 chr2D 91.277 321 22 4 4235 4550 239711352 239711033 3.350000e-117 433.0
3 TraesCS2D01G259800 chr2D 91.456 316 22 3 4235 4546 386504205 386503891 4.330000e-116 429.0
4 TraesCS2D01G259800 chr2D 89.888 178 15 3 5868 6045 5442187 5442013 6.100000e-55 226.0
5 TraesCS2D01G259800 chr2D 88.108 185 18 4 5681 5863 352948011 352947829 3.670000e-52 217.0
6 TraesCS2D01G259800 chr2B 94.984 2791 92 18 3080 5863 384037671 384034922 0.000000e+00 4335.0
7 TraesCS2D01G259800 chr2B 95.037 947 21 9 1759 2704 384038923 384038002 0.000000e+00 1465.0
8 TraesCS2D01G259800 chr2B 95.943 838 27 4 912 1749 384039736 384038906 0.000000e+00 1352.0
9 TraesCS2D01G259800 chr2B 89.256 484 29 2 422 884 384043859 384043378 8.730000e-163 584.0
10 TraesCS2D01G259800 chr2B 83.069 189 16 3 1 181 384045310 384045130 2.260000e-34 158.0
11 TraesCS2D01G259800 chr2B 78.879 232 37 9 328 553 94038231 94038006 4.880000e-31 147.0
12 TraesCS2D01G259800 chr2B 87.368 95 5 3 229 323 384044390 384044303 1.070000e-17 102.0
13 TraesCS2D01G259800 chr2A 94.514 1604 43 16 3800 5379 419030198 419031780 0.000000e+00 2433.0
14 TraesCS2D01G259800 chr2A 89.270 1808 94 41 2 1746 419026629 419028399 0.000000e+00 2172.0
15 TraesCS2D01G259800 chr2A 95.341 923 33 5 1759 2672 419028385 419029306 0.000000e+00 1458.0
16 TraesCS2D01G259800 chr2A 98.087 732 14 0 3070 3801 419029394 419030125 0.000000e+00 1275.0
17 TraesCS2D01G259800 chr2A 91.477 352 8 4 5346 5685 419031911 419032252 1.190000e-126 464.0
18 TraesCS2D01G259800 chr2A 91.713 181 10 4 5682 5859 696850891 696850713 4.680000e-61 246.0
19 TraesCS2D01G259800 chr2A 91.228 171 14 1 5687 5857 608605384 608605553 1.310000e-56 231.0
20 TraesCS2D01G259800 chr2A 81.250 224 40 2 329 551 519550129 519549907 4.820000e-41 180.0
21 TraesCS2D01G259800 chr2A 100.000 28 0 0 5347 5374 419031793 419031820 1.100000e-02 52.8
22 TraesCS2D01G259800 chr5B 91.875 320 20 4 4235 4550 394973746 394973429 5.560000e-120 442.0
23 TraesCS2D01G259800 chr5B 92.063 63 4 1 2260 2321 603239727 603239789 3.000000e-13 87.9
24 TraesCS2D01G259800 chr3B 91.304 322 21 5 4234 4549 342869637 342869957 3.350000e-117 433.0
25 TraesCS2D01G259800 chr3B 91.566 166 13 1 5692 5856 761137364 761137199 1.700000e-55 228.0
26 TraesCS2D01G259800 chr3B 77.729 229 47 4 327 553 145696345 145696571 2.940000e-28 137.0
27 TraesCS2D01G259800 chr3B 77.729 229 40 9 327 551 693472037 693472258 4.920000e-26 130.0
28 TraesCS2D01G259800 chr7B 91.277 321 21 3 4235 4550 446166208 446166526 1.200000e-116 431.0
29 TraesCS2D01G259800 chr7B 81.778 225 35 4 327 549 708423071 708422851 3.720000e-42 183.0
30 TraesCS2D01G259800 chr7B 76.068 234 43 8 327 551 36605328 36605557 6.410000e-20 110.0
31 TraesCS2D01G259800 chr7B 89.552 67 6 1 2268 2333 293977637 293977571 3.880000e-12 84.2
32 TraesCS2D01G259800 chr1D 91.022 323 23 4 4234 4551 180854699 180855020 1.200000e-116 431.0
33 TraesCS2D01G259800 chr1D 80.088 226 35 7 327 551 416877615 416877831 6.270000e-35 159.0
34 TraesCS2D01G259800 chr1D 91.379 58 4 1 2260 2316 221932834 221932891 1.810000e-10 78.7
35 TraesCS2D01G259800 chr1D 95.349 43 2 0 2274 2316 118886826 118886784 1.090000e-07 69.4
36 TraesCS2D01G259800 chr4D 90.994 322 21 5 4234 4550 304305053 304304735 1.560000e-115 427.0
37 TraesCS2D01G259800 chr4D 82.286 175 29 2 327 501 156143832 156143660 3.780000e-32 150.0
38 TraesCS2D01G259800 chr4D 91.667 60 5 0 2260 2319 428723894 428723953 3.880000e-12 84.2
39 TraesCS2D01G259800 chr4D 88.136 59 7 0 2260 2318 268079572 268079514 3.020000e-08 71.3
40 TraesCS2D01G259800 chr1A 90.000 330 23 8 4224 4547 208884139 208883814 9.370000e-113 418.0
41 TraesCS2D01G259800 chr1A 93.651 63 3 1 2268 2330 25707909 25707970 6.450000e-15 93.5
42 TraesCS2D01G259800 chr1A 87.879 66 7 1 2260 2325 399493483 399493419 6.500000e-10 76.8
43 TraesCS2D01G259800 chr1A 87.692 65 7 1 2260 2324 538399837 538399774 2.340000e-09 75.0
44 TraesCS2D01G259800 chr1A 88.333 60 7 0 2261 2320 119950587 119950528 8.410000e-09 73.1
45 TraesCS2D01G259800 chr4B 90.805 174 14 2 5694 5866 551728962 551728790 1.310000e-56 231.0
46 TraesCS2D01G259800 chr4B 90.805 174 14 2 5694 5866 551783568 551783396 1.310000e-56 231.0
47 TraesCS2D01G259800 chr4B 83.444 151 20 4 327 474 305786408 305786556 1.060000e-27 135.0
48 TraesCS2D01G259800 chr4B 76.106 226 51 3 327 550 200318993 200318769 1.380000e-21 115.0
49 TraesCS2D01G259800 chr4B 94.737 57 2 1 2268 2324 107660408 107660463 3.000000e-13 87.9
50 TraesCS2D01G259800 chr4B 91.803 61 5 0 2260 2320 193676416 193676476 1.080000e-12 86.1
51 TraesCS2D01G259800 chr4B 88.235 68 6 2 401 468 140919594 140919659 5.020000e-11 80.5
52 TraesCS2D01G259800 chr3A 90.395 177 10 6 5686 5860 375818232 375818403 6.100000e-55 226.0
53 TraesCS2D01G259800 chr3A 93.103 58 4 0 2260 2317 494032572 494032515 1.080000e-12 86.1
54 TraesCS2D01G259800 chr7A 89.385 179 16 3 5687 5864 677696240 677696416 7.890000e-54 222.0
55 TraesCS2D01G259800 chr7A 88.000 75 8 1 2260 2333 379906272 379906198 3.000000e-13 87.9
56 TraesCS2D01G259800 chr6B 82.902 193 27 6 327 518 669887071 669887258 1.040000e-37 169.0
57 TraesCS2D01G259800 chr6B 83.721 172 23 4 5868 6037 26121641 26121473 2.260000e-34 158.0
58 TraesCS2D01G259800 chr6B 82.166 157 25 3 326 481 497368003 497368157 1.370000e-26 132.0
59 TraesCS2D01G259800 chr6B 87.879 66 7 1 2260 2325 405902381 405902445 6.500000e-10 76.8
60 TraesCS2D01G259800 chr6B 87.879 66 7 1 2260 2325 682999678 682999614 6.500000e-10 76.8
61 TraesCS2D01G259800 chr6B 89.362 47 5 0 327 373 717716759 717716713 6.550000e-05 60.2
62 TraesCS2D01G259800 chrUn 77.434 226 46 3 327 551 84098276 84098055 4.920000e-26 130.0
63 TraesCS2D01G259800 chrUn 86.154 65 8 1 2260 2324 17536753 17536690 1.090000e-07 69.4
64 TraesCS2D01G259800 chr6A 80.952 147 21 6 323 467 535860337 535860478 6.410000e-20 110.0
65 TraesCS2D01G259800 chr6A 89.394 66 5 2 2260 2324 481235309 481235373 1.400000e-11 82.4
66 TraesCS2D01G259800 chr6A 87.931 58 7 0 2260 2317 554452264 554452321 1.090000e-07 69.4
67 TraesCS2D01G259800 chr6A 86.207 58 5 2 327 382 582959865 582959921 6.550000e-05 60.2
68 TraesCS2D01G259800 chr7D 93.443 61 4 0 2260 2320 601072534 601072594 2.320000e-14 91.6
69 TraesCS2D01G259800 chr7D 88.000 75 8 1 2260 2333 334831133 334831059 3.000000e-13 87.9
70 TraesCS2D01G259800 chr7D 79.032 124 24 2 352 475 58781514 58781635 3.880000e-12 84.2
71 TraesCS2D01G259800 chr3D 92.308 65 4 1 2260 2324 342716931 342716868 2.320000e-14 91.6
72 TraesCS2D01G259800 chr3D 93.443 61 4 0 2260 2320 414367641 414367701 2.320000e-14 91.6
73 TraesCS2D01G259800 chr4A 90.625 64 5 1 2260 2322 185435368 185435431 3.880000e-12 84.2
74 TraesCS2D01G259800 chr1B 90.323 62 6 0 2260 2321 157274598 157274659 1.400000e-11 82.4
75 TraesCS2D01G259800 chr5A 90.000 60 6 0 2260 2319 560568984 560568925 1.810000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G259800 chr2D 316121522 316127568 6046 True 5317.000000 5500 100.000000 1 6047 2 chr2D.!!$R5 6046
1 TraesCS2D01G259800 chr2B 384034922 384045310 10388 True 1332.666667 4335 90.942833 1 5863 6 chr2B.!!$R2 5862
2 TraesCS2D01G259800 chr2A 419026629 419032252 5623 False 1309.133333 2433 94.781500 2 5685 6 chr2A.!!$F2 5683

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
358 1062 0.803768 ACAGATGCAAGCGCTCGTAG 60.804 55.000 12.06 2.10 39.64 3.51 F
485 1559 0.809241 CCGTAGGCGTCTCGTAGTCT 60.809 60.000 0.00 0.00 46.14 3.24 F
1610 6339 0.037975 CCCATGTTGCTTGCTTCACC 60.038 55.000 0.00 0.00 0.00 4.02 F
1615 6344 1.340889 TGTTGCTTGCTTCACCCAATC 59.659 47.619 0.00 0.00 0.00 2.67 F
2741 7481 2.168106 AGGACAGCTATGAGCAACTCTG 59.832 50.000 0.64 0.00 45.56 3.35 F
3611 8355 0.110509 GCAGTGTTGCTGTCATGACG 60.111 55.000 20.54 15.64 46.95 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 6035 0.109342 ATATCTGAAAGCCCGGCAGG 59.891 55.000 13.15 0.0 39.47 4.85 R
1999 6728 0.528017 CGCTGACAGGAGCAGTTAGA 59.472 55.000 4.26 0.0 39.07 2.10 R
3579 8323 0.468226 ACACTGCCAGGAACGAAAGA 59.532 50.000 0.00 0.0 0.00 2.52 R
3611 8355 2.156098 TCAACGTTTGGGTATGCCTTC 58.844 47.619 0.00 0.0 34.45 3.46 R
4372 9198 0.980231 ACAAAGGGGGCAACAGCAAA 60.980 50.000 0.00 0.0 39.74 3.68 R
5607 10623 1.065031 GCAACGGCACTTACGCATTG 61.065 55.000 0.00 0.0 40.72 2.82 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 111 7.557036 CATGAACATGTACACAAACATTCAG 57.443 36.000 0.00 0.00 38.01 3.02
181 192 7.969536 AGTATCGCAACATTATAGCATTCTT 57.030 32.000 0.00 0.00 0.00 2.52
182 193 8.383318 AGTATCGCAACATTATAGCATTCTTT 57.617 30.769 0.00 0.00 0.00 2.52
184 195 9.450807 GTATCGCAACATTATAGCATTCTTTTT 57.549 29.630 0.00 0.00 0.00 1.94
225 911 7.994425 TCTATATTTCTCTGGAGTAGCAGAG 57.006 40.000 0.00 0.00 44.55 3.35
281 984 7.721286 TTTTAATTTTTGCGAATGACACCAT 57.279 28.000 0.00 0.00 33.66 3.55
325 1028 3.532138 CAACGAGCACTTGTTGGTG 57.468 52.632 19.07 0.00 46.26 4.17
355 1059 0.933097 AATACAGATGCAAGCGCTCG 59.067 50.000 12.06 0.00 39.64 5.03
358 1062 0.803768 ACAGATGCAAGCGCTCGTAG 60.804 55.000 12.06 2.10 39.64 3.51
369 1073 2.061773 GCGCTCGTAGATACATGCATT 58.938 47.619 0.00 0.00 33.89 3.56
392 1096 4.157289 TCACTCACCCTTATGAACGTACTC 59.843 45.833 0.00 0.00 0.00 2.59
395 1099 5.006153 TCACCCTTATGAACGTACTCATG 57.994 43.478 12.06 0.00 36.69 3.07
401 1108 5.445939 CCTTATGAACGTACTCATGCAACAC 60.446 44.000 12.06 0.00 36.69 3.32
405 1112 1.270274 ACGTACTCATGCAACACCGTA 59.730 47.619 0.00 0.00 0.00 4.02
418 1125 1.048601 CACCGTACCCCTATGAGCAT 58.951 55.000 0.00 0.00 0.00 3.79
431 1505 5.514659 CCCTATGAGCATCTCTGAGAGACTA 60.515 48.000 15.39 0.08 41.76 2.59
445 1519 2.297597 AGAGACTAAGCCGGCATATCAC 59.702 50.000 31.54 17.84 0.00 3.06
451 1525 3.290948 AAGCCGGCATATCACCTTAAA 57.709 42.857 31.54 0.00 0.00 1.52
458 1532 7.015195 AGCCGGCATATCACCTTAAAATTTTAT 59.985 33.333 31.54 0.00 0.00 1.40
485 1559 0.809241 CCGTAGGCGTCTCGTAGTCT 60.809 60.000 0.00 0.00 46.14 3.24
511 1585 6.258287 TCGAAAACGTCTTCTTCCATTAAACA 59.742 34.615 0.00 0.00 0.00 2.83
514 1588 4.374399 ACGTCTTCTTCCATTAAACACGT 58.626 39.130 0.00 0.00 33.35 4.49
518 1592 6.309494 CGTCTTCTTCCATTAAACACGTATCA 59.691 38.462 0.00 0.00 0.00 2.15
520 1594 7.117236 GTCTTCTTCCATTAAACACGTATCACA 59.883 37.037 0.00 0.00 0.00 3.58
740 1847 1.338579 GCTCCTCTTTCCACCTCACAG 60.339 57.143 0.00 0.00 0.00 3.66
783 1890 2.207229 CCCCACTCACAGGTCGACA 61.207 63.158 18.91 0.00 0.00 4.35
885 1992 4.380841 TCTTCCTCGCTCGCTTTATAAA 57.619 40.909 0.00 0.00 0.00 1.40
1306 6035 1.084370 CGGGCTGATTCGGTGTCTTC 61.084 60.000 0.00 0.00 0.00 2.87
1366 6095 2.887568 GCGGTGGTGATCTCGCTG 60.888 66.667 0.00 0.00 44.10 5.18
1387 6116 4.131088 GTGGCCGTCCTCGAGACC 62.131 72.222 15.71 7.67 43.08 3.85
1426 6155 3.818210 TCAAATTCTGCAAGGTTCGCTTA 59.182 39.130 0.00 0.00 0.00 3.09
1427 6156 4.277174 TCAAATTCTGCAAGGTTCGCTTAA 59.723 37.500 0.00 0.00 0.00 1.85
1433 6162 1.067915 GCAAGGTTCGCTTAATTGCCA 60.068 47.619 0.00 0.00 40.20 4.92
1593 6322 2.037847 AGCCTCCAAATGGTGCCC 59.962 61.111 11.33 0.00 35.62 5.36
1610 6339 0.037975 CCCATGTTGCTTGCTTCACC 60.038 55.000 0.00 0.00 0.00 4.02
1615 6344 1.340889 TGTTGCTTGCTTCACCCAATC 59.659 47.619 0.00 0.00 0.00 2.67
1628 6357 5.798125 TCACCCAATCAATTGTTTGCTAA 57.202 34.783 19.52 5.98 36.06 3.09
1655 6384 9.673454 CATTCATTGATAGTGGAATGTGTTATG 57.327 33.333 0.00 0.00 40.89 1.90
1785 6514 9.999009 GATGCCATGTCATTATTATAGTGAATG 57.001 33.333 0.00 6.15 32.85 2.67
1786 6515 9.743581 ATGCCATGTCATTATTATAGTGAATGA 57.256 29.630 14.70 0.00 37.27 2.57
1806 6535 6.705863 ATGATCAGATTGTCCTTTTAAGGC 57.294 37.500 0.09 0.62 46.06 4.35
1816 6545 6.327386 TGTCCTTTTAAGGCCATCTCTTAT 57.673 37.500 5.01 0.00 46.06 1.73
1820 6549 5.536538 CCTTTTAAGGCCATCTCTTATTCCC 59.463 44.000 5.01 0.00 39.76 3.97
1850 6579 6.049790 GTGTAATCTTAAGTTGCCTCTAGGG 58.950 44.000 1.63 0.00 35.18 3.53
1941 6670 5.948992 ACATACAAACTTGCTCTCTTTCC 57.051 39.130 0.00 0.00 0.00 3.13
1999 6728 4.020218 TGATGACGGAACTTTGGAGATTCT 60.020 41.667 0.00 0.00 0.00 2.40
2037 6766 4.213270 CAGCGAACACCAAGTCTTATTTCA 59.787 41.667 0.00 0.00 0.00 2.69
2347 7078 9.566432 TTTTTACTGGAATTGGTGCATATTTTT 57.434 25.926 0.00 0.00 0.00 1.94
2382 7113 7.420002 TCAGAATGTTTCATGCATATGCTTAC 58.580 34.615 27.13 16.32 38.73 2.34
2386 7117 6.122850 TGTTTCATGCATATGCTTACTGTC 57.877 37.500 27.13 12.99 42.66 3.51
2387 7118 5.200454 GTTTCATGCATATGCTTACTGTCG 58.800 41.667 27.13 9.20 42.66 4.35
2388 7119 3.392882 TCATGCATATGCTTACTGTCGG 58.607 45.455 27.13 8.55 42.66 4.79
2508 7248 5.574188 AGAGGTGTGGCTTCATAATTTTCT 58.426 37.500 0.00 0.00 0.00 2.52
2639 7379 9.964303 CCTTAAGCATAGCTATGACATATAGAG 57.036 37.037 33.10 18.18 38.25 2.43
2715 7455 6.852664 AGCAAATTGGCTGTACTATTACAAC 58.147 36.000 6.51 0.00 43.89 3.32
2716 7456 6.432783 AGCAAATTGGCTGTACTATTACAACA 59.567 34.615 6.51 0.00 43.89 3.33
2717 7457 6.747280 GCAAATTGGCTGTACTATTACAACAG 59.253 38.462 0.00 0.00 42.80 3.16
2718 7458 7.361713 GCAAATTGGCTGTACTATTACAACAGA 60.362 37.037 0.00 0.00 42.59 3.41
2719 7459 8.511321 CAAATTGGCTGTACTATTACAACAGAA 58.489 33.333 5.91 0.00 42.59 3.02
2720 7460 8.630054 AATTGGCTGTACTATTACAACAGAAA 57.370 30.769 5.91 0.46 42.59 2.52
2721 7461 7.667043 TTGGCTGTACTATTACAACAGAAAG 57.333 36.000 5.91 0.00 42.59 2.62
2722 7462 6.170506 TGGCTGTACTATTACAACAGAAAGG 58.829 40.000 5.91 0.00 42.59 3.11
2723 7463 6.014070 TGGCTGTACTATTACAACAGAAAGGA 60.014 38.462 5.91 0.00 42.59 3.36
2724 7464 6.313164 GGCTGTACTATTACAACAGAAAGGAC 59.687 42.308 5.91 0.00 42.59 3.85
2727 7467 6.872020 TGTACTATTACAACAGAAAGGACAGC 59.128 38.462 0.00 0.00 35.14 4.40
2728 7468 6.115448 ACTATTACAACAGAAAGGACAGCT 57.885 37.500 0.00 0.00 0.00 4.24
2729 7469 7.241042 ACTATTACAACAGAAAGGACAGCTA 57.759 36.000 0.00 0.00 0.00 3.32
2731 7471 6.992063 ATTACAACAGAAAGGACAGCTATG 57.008 37.500 0.00 0.00 0.00 2.23
2732 7472 4.623932 ACAACAGAAAGGACAGCTATGA 57.376 40.909 0.00 0.00 0.00 2.15
2733 7473 4.573900 ACAACAGAAAGGACAGCTATGAG 58.426 43.478 0.00 0.00 0.00 2.90
2734 7474 3.258971 ACAGAAAGGACAGCTATGAGC 57.741 47.619 0.00 0.00 42.84 4.26
2735 7475 2.568956 ACAGAAAGGACAGCTATGAGCA 59.431 45.455 0.64 0.00 45.56 4.26
2737 7477 3.373439 CAGAAAGGACAGCTATGAGCAAC 59.627 47.826 0.64 0.00 45.56 4.17
2738 7478 3.262915 AGAAAGGACAGCTATGAGCAACT 59.737 43.478 0.64 0.00 45.56 3.16
2739 7479 2.977772 AGGACAGCTATGAGCAACTC 57.022 50.000 0.64 0.00 45.56 3.01
2740 7480 2.465813 AGGACAGCTATGAGCAACTCT 58.534 47.619 0.64 0.00 45.56 3.24
2741 7481 2.168106 AGGACAGCTATGAGCAACTCTG 59.832 50.000 0.64 0.00 45.56 3.35
2742 7482 2.548875 GACAGCTATGAGCAACTCTGG 58.451 52.381 0.64 0.00 45.56 3.86
3231 7975 3.560025 CCAGGGTGACTAGAAATGCAAGT 60.560 47.826 0.00 0.00 0.00 3.16
3386 8130 3.500455 GCATTCACAGCACATGCAA 57.500 47.368 6.64 0.00 42.49 4.08
3446 8190 3.941704 ATTCTGGGATCCTGAACCTTC 57.058 47.619 12.58 0.00 42.56 3.46
3611 8355 0.110509 GCAGTGTTGCTGTCATGACG 60.111 55.000 20.54 15.64 46.95 4.35
4256 9081 7.119699 AGTGTGTTGAAGTGTATATGTGGATTG 59.880 37.037 0.00 0.00 0.00 2.67
4316 9142 4.333649 GCTAGTGCATGAAGCTTTACATGA 59.666 41.667 24.80 11.84 44.28 3.07
4330 9156 5.578727 GCTTTACATGATATCGGAGCCTAAG 59.421 44.000 0.00 0.00 0.00 2.18
4331 9157 3.601443 ACATGATATCGGAGCCTAAGC 57.399 47.619 0.00 0.00 40.32 3.09
4379 9205 7.507733 TGCAATTTATCCAAAAATTTGCTGT 57.492 28.000 13.36 0.00 37.03 4.40
4430 9279 4.402829 TGAGCCATACCTCTGAGTCTATC 58.597 47.826 3.66 0.00 33.02 2.08
4524 9373 5.598005 TCCATCAGTTTGGACTTTTGATTGT 59.402 36.000 0.00 0.00 40.90 2.71
4561 9410 7.043059 GCATGAAGCTTAACAGAGTGTATACTC 60.043 40.741 11.43 11.43 45.91 2.59
4621 9470 1.740380 CGTGGTTCCTGCCTGATAGTG 60.740 57.143 0.00 0.00 0.00 2.74
4625 9474 3.181434 TGGTTCCTGCCTGATAGTGTTTT 60.181 43.478 0.00 0.00 0.00 2.43
4725 9574 2.706890 TGGTATGAAGGTTTTCCGAGC 58.293 47.619 0.00 0.00 46.35 5.03
4922 9771 8.369424 TCAAGGCTACAGTTTACAACAATAGTA 58.631 33.333 0.00 0.00 0.00 1.82
4950 9799 3.305608 CGCTACCATGATGTCATCTGCTA 60.306 47.826 13.90 0.00 33.61 3.49
5182 10032 0.178961 GAGTGCCCCCTTTTCCTGTT 60.179 55.000 0.00 0.00 0.00 3.16
5189 10039 2.162681 CCCCTTTTCCTGTTAGTGCTG 58.837 52.381 0.00 0.00 0.00 4.41
5246 10096 1.093972 TTGCAGTGGACCATATTGCG 58.906 50.000 18.08 0.00 37.58 4.85
5251 10101 1.210478 AGTGGACCATATTGCGCTCTT 59.790 47.619 9.73 0.00 0.00 2.85
5478 10484 6.312918 GTGTTTGTTGTCTCTGTAGTCTTTGA 59.687 38.462 0.00 0.00 0.00 2.69
5528 10534 9.802039 TTTCTGTATTTTGTGTAATAGAGGGTT 57.198 29.630 0.00 0.00 34.09 4.11
5607 10623 4.080638 AGAGTTGGGATTCTTGATCTGGAC 60.081 45.833 0.00 0.00 35.02 4.02
5703 10719 9.938280 TGTATATGAAAAATATTACTCCCTCCG 57.062 33.333 0.00 0.00 0.00 4.63
5809 10825 7.434897 CACTGATTTTGCTCTCTATGTAGTCTC 59.565 40.741 0.00 0.00 0.00 3.36
5816 10832 7.517614 TGCTCTCTATGTAGTCTCTTATTGG 57.482 40.000 0.00 0.00 0.00 3.16
5863 10879 5.982391 AGGAATGGAGGGAGTATCTTCATA 58.018 41.667 0.00 0.00 33.73 2.15
5864 10880 6.022315 AGGAATGGAGGGAGTATCTTCATAG 58.978 44.000 0.00 0.00 33.73 2.23
5865 10881 6.019748 GGAATGGAGGGAGTATCTTCATAGA 58.980 44.000 0.00 0.00 33.73 1.98
5866 10882 6.071051 GGAATGGAGGGAGTATCTTCATAGAC 60.071 46.154 0.00 0.00 31.99 2.59
5867 10883 5.671463 TGGAGGGAGTATCTTCATAGACT 57.329 43.478 0.00 0.00 31.99 3.24
5868 10884 6.031964 TGGAGGGAGTATCTTCATAGACTT 57.968 41.667 0.00 0.00 31.99 3.01
5869 10885 7.162973 TGGAGGGAGTATCTTCATAGACTTA 57.837 40.000 0.00 0.00 31.99 2.24
5870 10886 7.235079 TGGAGGGAGTATCTTCATAGACTTAG 58.765 42.308 0.00 0.00 31.99 2.18
5871 10887 6.661805 GGAGGGAGTATCTTCATAGACTTAGG 59.338 46.154 0.00 0.00 31.99 2.69
5872 10888 6.557568 AGGGAGTATCTTCATAGACTTAGGG 58.442 44.000 0.00 0.00 31.99 3.53
5873 10889 5.717654 GGGAGTATCTTCATAGACTTAGGGG 59.282 48.000 0.00 0.00 31.99 4.79
5874 10890 5.717654 GGAGTATCTTCATAGACTTAGGGGG 59.282 48.000 0.00 0.00 31.99 5.40
5875 10891 6.296435 AGTATCTTCATAGACTTAGGGGGT 57.704 41.667 0.00 0.00 31.99 4.95
5876 10892 6.078664 AGTATCTTCATAGACTTAGGGGGTG 58.921 44.000 0.00 0.00 31.99 4.61
5877 10893 4.348020 TCTTCATAGACTTAGGGGGTGT 57.652 45.455 0.00 0.00 0.00 4.16
5878 10894 4.695606 TCTTCATAGACTTAGGGGGTGTT 58.304 43.478 0.00 0.00 0.00 3.32
5879 10895 4.715297 TCTTCATAGACTTAGGGGGTGTTC 59.285 45.833 0.00 0.00 0.00 3.18
5880 10896 3.028850 TCATAGACTTAGGGGGTGTTCG 58.971 50.000 0.00 0.00 0.00 3.95
5881 10897 1.856629 TAGACTTAGGGGGTGTTCGG 58.143 55.000 0.00 0.00 0.00 4.30
5882 10898 0.178912 AGACTTAGGGGGTGTTCGGT 60.179 55.000 0.00 0.00 0.00 4.69
5883 10899 0.689055 GACTTAGGGGGTGTTCGGTT 59.311 55.000 0.00 0.00 0.00 4.44
5884 10900 0.399075 ACTTAGGGGGTGTTCGGTTG 59.601 55.000 0.00 0.00 0.00 3.77
5885 10901 0.958876 CTTAGGGGGTGTTCGGTTGC 60.959 60.000 0.00 0.00 0.00 4.17
5886 10902 1.706995 TTAGGGGGTGTTCGGTTGCA 61.707 55.000 0.00 0.00 0.00 4.08
5887 10903 2.400269 TAGGGGGTGTTCGGTTGCAC 62.400 60.000 0.00 0.00 35.07 4.57
5888 10904 3.656045 GGGGTGTTCGGTTGCACG 61.656 66.667 0.00 0.00 36.54 5.34
5889 10905 3.656045 GGGTGTTCGGTTGCACGG 61.656 66.667 0.00 0.00 36.54 4.94
5890 10906 3.656045 GGTGTTCGGTTGCACGGG 61.656 66.667 0.00 0.00 36.54 5.28
5891 10907 2.589442 GTGTTCGGTTGCACGGGA 60.589 61.111 0.00 0.00 0.00 5.14
5892 10908 2.589442 TGTTCGGTTGCACGGGAC 60.589 61.111 0.00 0.00 0.00 4.46
5893 10909 2.280592 GTTCGGTTGCACGGGACT 60.281 61.111 0.00 0.00 0.00 3.85
5894 10910 1.005867 GTTCGGTTGCACGGGACTA 60.006 57.895 0.00 0.00 0.00 2.59
5895 10911 0.390735 GTTCGGTTGCACGGGACTAT 60.391 55.000 0.00 0.00 0.00 2.12
5896 10912 0.390603 TTCGGTTGCACGGGACTATG 60.391 55.000 0.00 0.00 0.00 2.23
5897 10913 1.216977 CGGTTGCACGGGACTATGA 59.783 57.895 0.00 0.00 0.00 2.15
5898 10914 0.390603 CGGTTGCACGGGACTATGAA 60.391 55.000 0.00 0.00 0.00 2.57
5899 10915 1.084289 GGTTGCACGGGACTATGAAC 58.916 55.000 0.00 0.00 0.00 3.18
5900 10916 1.338769 GGTTGCACGGGACTATGAACT 60.339 52.381 0.00 0.00 0.00 3.01
5901 10917 2.423577 GTTGCACGGGACTATGAACTT 58.576 47.619 0.00 0.00 0.00 2.66
5902 10918 2.812011 GTTGCACGGGACTATGAACTTT 59.188 45.455 0.00 0.00 0.00 2.66
5903 10919 3.134574 TGCACGGGACTATGAACTTTT 57.865 42.857 0.00 0.00 0.00 2.27
5904 10920 3.482436 TGCACGGGACTATGAACTTTTT 58.518 40.909 0.00 0.00 0.00 1.94
5951 10967 9.642343 AAAAATACCCTTCAGTAGAGTCTTTTT 57.358 29.630 0.00 0.00 0.00 1.94
5952 10968 8.850007 AAATACCCTTCAGTAGAGTCTTTTTC 57.150 34.615 0.00 0.00 0.00 2.29
5953 10969 7.800300 ATACCCTTCAGTAGAGTCTTTTTCT 57.200 36.000 0.00 0.00 0.00 2.52
5954 10970 8.896722 ATACCCTTCAGTAGAGTCTTTTTCTA 57.103 34.615 0.00 0.00 0.00 2.10
5955 10971 7.613551 ACCCTTCAGTAGAGTCTTTTTCTAA 57.386 36.000 0.00 0.00 0.00 2.10
5956 10972 8.208575 ACCCTTCAGTAGAGTCTTTTTCTAAT 57.791 34.615 0.00 0.00 0.00 1.73
5957 10973 8.315482 ACCCTTCAGTAGAGTCTTTTTCTAATC 58.685 37.037 0.00 0.00 0.00 1.75
5958 10974 7.766738 CCCTTCAGTAGAGTCTTTTTCTAATCC 59.233 40.741 0.00 0.00 0.00 3.01
5959 10975 7.766738 CCTTCAGTAGAGTCTTTTTCTAATCCC 59.233 40.741 0.00 0.00 0.00 3.85
5960 10976 8.437274 TTCAGTAGAGTCTTTTTCTAATCCCT 57.563 34.615 0.00 0.00 0.00 4.20
5961 10977 9.543231 TTCAGTAGAGTCTTTTTCTAATCCCTA 57.457 33.333 0.00 0.00 0.00 3.53
5962 10978 9.543231 TCAGTAGAGTCTTTTTCTAATCCCTAA 57.457 33.333 0.00 0.00 0.00 2.69
5974 10990 9.524496 TTTTCTAATCCCTAAAGTAAAAGTCCC 57.476 33.333 0.00 0.00 0.00 4.46
5975 10991 8.458951 TTCTAATCCCTAAAGTAAAAGTCCCT 57.541 34.615 0.00 0.00 0.00 4.20
5976 10992 8.087303 TCTAATCCCTAAAGTAAAAGTCCCTC 57.913 38.462 0.00 0.00 0.00 4.30
5977 10993 5.712084 ATCCCTAAAGTAAAAGTCCCTCC 57.288 43.478 0.00 0.00 0.00 4.30
5978 10994 4.771338 TCCCTAAAGTAAAAGTCCCTCCT 58.229 43.478 0.00 0.00 0.00 3.69
5979 10995 4.534897 TCCCTAAAGTAAAAGTCCCTCCTG 59.465 45.833 0.00 0.00 0.00 3.86
5980 10996 4.288887 CCCTAAAGTAAAAGTCCCTCCTGT 59.711 45.833 0.00 0.00 0.00 4.00
5981 10997 5.222068 CCCTAAAGTAAAAGTCCCTCCTGTT 60.222 44.000 0.00 0.00 0.00 3.16
5982 10998 6.304624 CCTAAAGTAAAAGTCCCTCCTGTTT 58.695 40.000 0.00 0.00 0.00 2.83
5983 10999 6.206829 CCTAAAGTAAAAGTCCCTCCTGTTTG 59.793 42.308 0.00 0.00 0.00 2.93
5984 11000 5.382664 AAGTAAAAGTCCCTCCTGTTTGA 57.617 39.130 0.00 0.00 0.00 2.69
5985 11001 5.584551 AGTAAAAGTCCCTCCTGTTTGAT 57.415 39.130 0.00 0.00 0.00 2.57
5986 11002 5.953571 AGTAAAAGTCCCTCCTGTTTGATT 58.046 37.500 0.00 0.00 0.00 2.57
5987 11003 7.086685 AGTAAAAGTCCCTCCTGTTTGATTA 57.913 36.000 0.00 0.00 0.00 1.75
5988 11004 6.940867 AGTAAAAGTCCCTCCTGTTTGATTAC 59.059 38.462 0.00 0.00 0.00 1.89
5989 11005 4.993705 AAGTCCCTCCTGTTTGATTACA 57.006 40.909 0.00 0.00 0.00 2.41
5990 11006 5.520748 AAGTCCCTCCTGTTTGATTACAT 57.479 39.130 0.00 0.00 0.00 2.29
5991 11007 6.636454 AAGTCCCTCCTGTTTGATTACATA 57.364 37.500 0.00 0.00 0.00 2.29
5992 11008 6.240549 AGTCCCTCCTGTTTGATTACATAG 57.759 41.667 0.00 0.00 0.00 2.23
5993 11009 5.131142 AGTCCCTCCTGTTTGATTACATAGG 59.869 44.000 0.00 0.00 33.80 2.57
5994 11010 4.412199 TCCCTCCTGTTTGATTACATAGGG 59.588 45.833 13.94 13.94 44.71 3.53
5995 11011 4.412199 CCCTCCTGTTTGATTACATAGGGA 59.588 45.833 14.57 2.23 45.42 4.20
5996 11012 5.073691 CCCTCCTGTTTGATTACATAGGGAT 59.926 44.000 14.57 0.00 45.42 3.85
5997 11013 6.410853 CCCTCCTGTTTGATTACATAGGGATT 60.411 42.308 14.57 0.00 45.42 3.01
5998 11014 7.202186 CCCTCCTGTTTGATTACATAGGGATTA 60.202 40.741 14.57 0.00 45.42 1.75
5999 11015 8.217799 CCTCCTGTTTGATTACATAGGGATTAA 58.782 37.037 0.00 0.00 31.92 1.40
6000 11016 9.627123 CTCCTGTTTGATTACATAGGGATTAAA 57.373 33.333 0.00 0.00 0.00 1.52
6001 11017 9.983024 TCCTGTTTGATTACATAGGGATTAAAA 57.017 29.630 0.00 0.00 0.00 1.52
6007 11023 9.847224 TTGATTACATAGGGATTAAAAGAGACC 57.153 33.333 0.00 0.00 0.00 3.85
6008 11024 9.225682 TGATTACATAGGGATTAAAAGAGACCT 57.774 33.333 0.00 0.00 0.00 3.85
6012 11028 8.809468 ACATAGGGATTAAAAGAGACCTTTTC 57.191 34.615 6.44 0.00 46.49 2.29
6013 11029 8.615705 ACATAGGGATTAAAAGAGACCTTTTCT 58.384 33.333 6.44 1.65 46.49 2.52
6017 11033 9.688091 AGGGATTAAAAGAGACCTTTTCTAATC 57.312 33.333 6.44 10.38 46.49 1.75
6018 11034 9.688091 GGGATTAAAAGAGACCTTTTCTAATCT 57.312 33.333 16.97 0.00 46.49 2.40
6024 11040 8.840833 AAAGAGACCTTTTCTAATCTTGTCTC 57.159 34.615 8.33 8.33 44.64 3.36
6026 11042 7.826260 GAGACCTTTTCTAATCTTGTCTCTG 57.174 40.000 8.96 0.00 42.33 3.35
6027 11043 7.309770 AGACCTTTTCTAATCTTGTCTCTGT 57.690 36.000 0.00 0.00 30.17 3.41
6028 11044 8.423906 AGACCTTTTCTAATCTTGTCTCTGTA 57.576 34.615 0.00 0.00 30.17 2.74
6029 11045 8.871125 AGACCTTTTCTAATCTTGTCTCTGTAA 58.129 33.333 0.00 0.00 30.17 2.41
6030 11046 8.834749 ACCTTTTCTAATCTTGTCTCTGTAAC 57.165 34.615 0.00 0.00 0.00 2.50
6031 11047 7.878644 ACCTTTTCTAATCTTGTCTCTGTAACC 59.121 37.037 0.00 0.00 0.00 2.85
6032 11048 7.878127 CCTTTTCTAATCTTGTCTCTGTAACCA 59.122 37.037 0.00 0.00 0.00 3.67
6033 11049 9.273016 CTTTTCTAATCTTGTCTCTGTAACCAA 57.727 33.333 0.00 0.00 0.00 3.67
6034 11050 9.621629 TTTTCTAATCTTGTCTCTGTAACCAAA 57.378 29.630 0.00 0.00 0.00 3.28
6035 11051 8.603242 TTCTAATCTTGTCTCTGTAACCAAAC 57.397 34.615 0.00 0.00 0.00 2.93
6036 11052 7.732025 TCTAATCTTGTCTCTGTAACCAAACA 58.268 34.615 0.00 0.00 0.00 2.83
6037 11053 6.867662 AATCTTGTCTCTGTAACCAAACAG 57.132 37.500 0.00 0.00 46.78 3.16
6038 11054 4.703897 TCTTGTCTCTGTAACCAAACAGG 58.296 43.478 4.32 0.00 45.69 4.00
6040 11056 2.152016 GTCTCTGTAACCAAACAGGGC 58.848 52.381 4.32 0.00 45.87 5.19
6041 11057 1.073284 TCTCTGTAACCAAACAGGGCC 59.927 52.381 0.00 0.00 45.87 5.80
6042 11058 1.073923 CTCTGTAACCAAACAGGGCCT 59.926 52.381 0.00 0.00 45.69 5.19
6043 11059 1.497286 TCTGTAACCAAACAGGGCCTT 59.503 47.619 1.32 0.00 45.69 4.35
6044 11060 2.712087 TCTGTAACCAAACAGGGCCTTA 59.288 45.455 1.32 0.00 45.69 2.69
6045 11061 3.332485 TCTGTAACCAAACAGGGCCTTAT 59.668 43.478 1.32 0.00 45.69 1.73
6046 11062 4.536888 TCTGTAACCAAACAGGGCCTTATA 59.463 41.667 1.32 0.00 45.69 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 31 6.978338 TGTGAAACGAGATAGTAGTGTTTCT 58.022 36.000 14.76 0.00 45.25 2.52
160 171 8.190122 TGAAAAAGAATGCTATAATGTTGCGAT 58.810 29.630 0.00 0.00 0.00 4.58
162 173 7.739022 TGAAAAAGAATGCTATAATGTTGCG 57.261 32.000 0.00 0.00 0.00 4.85
214 900 5.703130 ACTGAACAAAAATCTCTGCTACTCC 59.297 40.000 0.00 0.00 0.00 3.85
225 911 6.060028 TGCTAGTGTCACTGAACAAAAATC 57.940 37.500 16.03 0.00 0.00 2.17
262 965 4.517952 TGATGGTGTCATTCGCAAAAAT 57.482 36.364 0.00 0.00 32.98 1.82
309 1012 1.459450 AAACACCAACAAGTGCTCGT 58.541 45.000 0.00 0.00 41.67 4.18
324 1027 7.168972 GCTTGCATCTGTATTGTGTTAAAAACA 59.831 33.333 0.00 0.00 39.52 2.83
325 1028 7.501515 GCTTGCATCTGTATTGTGTTAAAAAC 58.498 34.615 0.00 0.00 0.00 2.43
340 1044 0.526310 TCTACGAGCGCTTGCATCTG 60.526 55.000 24.80 10.10 42.66 2.90
355 1059 4.752101 GGGTGAGTGAATGCATGTATCTAC 59.248 45.833 0.00 0.00 0.00 2.59
358 1062 3.813443 AGGGTGAGTGAATGCATGTATC 58.187 45.455 0.00 0.00 0.00 2.24
369 1073 4.084287 AGTACGTTCATAAGGGTGAGTGA 58.916 43.478 0.00 0.00 0.00 3.41
392 1096 0.250793 TAGGGGTACGGTGTTGCATG 59.749 55.000 0.00 0.00 0.00 4.06
395 1099 0.538118 TCATAGGGGTACGGTGTTGC 59.462 55.000 0.00 0.00 0.00 4.17
401 1108 1.546476 GAGATGCTCATAGGGGTACGG 59.454 57.143 0.00 0.00 0.00 4.02
405 1112 2.178764 TCTCAGAGATGCTCATAGGGGT 59.821 50.000 0.00 0.00 32.06 4.95
418 1125 2.019668 GCCGGCTTAGTCTCTCAGAGA 61.020 57.143 22.15 0.00 36.22 3.10
431 1505 3.290948 TTTAAGGTGATATGCCGGCTT 57.709 42.857 29.70 24.47 0.00 4.35
445 1519 9.769093 CTACGGTGACTTCATAAAATTTTAAGG 57.231 33.333 14.35 9.97 0.00 2.69
451 1525 4.331717 CGCCTACGGTGACTTCATAAAATT 59.668 41.667 0.00 0.00 34.74 1.82
458 1532 0.892358 AGACGCCTACGGTGACTTCA 60.892 55.000 0.00 0.00 46.04 3.02
472 1546 2.238245 TTTCGAAGACTACGAGACGC 57.762 50.000 0.00 0.00 40.72 5.19
473 1547 2.582946 CGTTTTCGAAGACTACGAGACG 59.417 50.000 15.88 0.00 43.37 4.18
476 1550 3.808095 AGACGTTTTCGAAGACTACGAG 58.192 45.455 22.16 9.20 43.37 4.18
885 1992 0.887836 TGTGAGGTGTACGAGCGAGT 60.888 55.000 0.00 0.00 0.00 4.18
1306 6035 0.109342 ATATCTGAAAGCCCGGCAGG 59.891 55.000 13.15 0.00 39.47 4.85
1387 6116 2.916702 TGATGATGAATCCCCACTCG 57.083 50.000 0.00 0.00 34.00 4.18
1593 6322 0.675083 TGGGTGAAGCAAGCAACATG 59.325 50.000 0.00 0.00 0.00 3.21
1651 6380 6.988622 ATTAAAATTCCGACACCGACATAA 57.011 33.333 0.00 0.00 38.22 1.90
1655 6384 4.083164 ACCAATTAAAATTCCGACACCGAC 60.083 41.667 0.00 0.00 38.22 4.79
1747 6476 4.037327 TGACATGGCATCTTCGTTCAAAAA 59.963 37.500 0.00 0.00 0.00 1.94
1748 6477 3.567585 TGACATGGCATCTTCGTTCAAAA 59.432 39.130 0.00 0.00 0.00 2.44
1749 6478 3.145286 TGACATGGCATCTTCGTTCAAA 58.855 40.909 0.00 0.00 0.00 2.69
1750 6479 2.777094 TGACATGGCATCTTCGTTCAA 58.223 42.857 0.00 0.00 0.00 2.69
1751 6480 2.470983 TGACATGGCATCTTCGTTCA 57.529 45.000 0.00 0.00 0.00 3.18
1752 6481 5.679734 ATAATGACATGGCATCTTCGTTC 57.320 39.130 16.14 0.00 0.00 3.95
1753 6482 7.750229 ATAATAATGACATGGCATCTTCGTT 57.250 32.000 16.14 14.46 0.00 3.85
1754 6483 8.097038 ACTATAATAATGACATGGCATCTTCGT 58.903 33.333 16.14 0.43 0.00 3.85
1755 6484 8.385858 CACTATAATAATGACATGGCATCTTCG 58.614 37.037 16.14 6.78 0.00 3.79
1756 6485 9.440773 TCACTATAATAATGACATGGCATCTTC 57.559 33.333 16.14 0.00 0.00 2.87
1757 6486 9.797642 TTCACTATAATAATGACATGGCATCTT 57.202 29.630 16.14 13.89 0.00 2.40
1806 6535 5.688807 ACACTCAATGGGAATAAGAGATGG 58.311 41.667 0.00 0.00 0.00 3.51
1816 6545 7.094377 GCAACTTAAGATTACACTCAATGGGAA 60.094 37.037 10.09 0.00 0.00 3.97
1850 6579 4.636249 CAAGCCTGTATATTCTGTCTCCC 58.364 47.826 0.00 0.00 0.00 4.30
1999 6728 0.528017 CGCTGACAGGAGCAGTTAGA 59.472 55.000 4.26 0.00 39.07 2.10
2037 6766 4.242336 AGCTTAAATCTAAAGGGCAGCT 57.758 40.909 0.00 0.00 0.00 4.24
2311 7040 7.017155 ACCAATTCCAGTAAAAATAAAAGGGCT 59.983 33.333 0.00 0.00 0.00 5.19
2347 7078 7.978414 TGCATGAAACATTCTGAAAAACTGTAA 59.022 29.630 0.00 0.00 0.00 2.41
2348 7079 7.487484 TGCATGAAACATTCTGAAAAACTGTA 58.513 30.769 0.00 0.00 0.00 2.74
2352 7083 7.901377 GCATATGCATGAAACATTCTGAAAAAC 59.099 33.333 22.84 0.00 41.59 2.43
2382 7113 2.020720 ACTCTAGATGAGCACCGACAG 58.979 52.381 0.00 0.00 46.41 3.51
2386 7117 3.381908 AGGTAAACTCTAGATGAGCACCG 59.618 47.826 0.00 0.00 46.41 4.94
2387 7118 6.658188 ATAGGTAAACTCTAGATGAGCACC 57.342 41.667 0.00 0.00 46.41 5.01
2429 7169 5.948742 ACTTCCAAAAATGAAGGAACCAA 57.051 34.783 5.16 0.00 42.79 3.67
2508 7248 7.925483 CCACAATTTTCAAGAACCATTCAGTTA 59.075 33.333 0.00 0.00 0.00 2.24
2639 7379 4.045636 AGGTTTGTGTTTGTCATGCTTC 57.954 40.909 0.00 0.00 0.00 3.86
2704 7444 7.241042 AGCTGTCCTTTCTGTTGTAATAGTA 57.759 36.000 0.00 0.00 0.00 1.82
2705 7445 6.115448 AGCTGTCCTTTCTGTTGTAATAGT 57.885 37.500 0.00 0.00 0.00 2.12
2706 7446 7.981789 TCATAGCTGTCCTTTCTGTTGTAATAG 59.018 37.037 0.00 0.00 0.00 1.73
2707 7447 7.847096 TCATAGCTGTCCTTTCTGTTGTAATA 58.153 34.615 0.00 0.00 0.00 0.98
2708 7448 6.711277 TCATAGCTGTCCTTTCTGTTGTAAT 58.289 36.000 0.00 0.00 0.00 1.89
2709 7449 6.109156 TCATAGCTGTCCTTTCTGTTGTAA 57.891 37.500 0.00 0.00 0.00 2.41
2711 7451 4.573900 CTCATAGCTGTCCTTTCTGTTGT 58.426 43.478 0.00 0.00 0.00 3.32
2714 7454 2.568956 TGCTCATAGCTGTCCTTTCTGT 59.431 45.455 0.00 0.00 42.97 3.41
2715 7455 3.257469 TGCTCATAGCTGTCCTTTCTG 57.743 47.619 0.00 0.00 42.97 3.02
2716 7456 3.262915 AGTTGCTCATAGCTGTCCTTTCT 59.737 43.478 0.00 0.00 42.97 2.52
2717 7457 3.604582 AGTTGCTCATAGCTGTCCTTTC 58.395 45.455 0.00 0.00 42.97 2.62
2718 7458 3.262915 AGAGTTGCTCATAGCTGTCCTTT 59.737 43.478 0.00 0.00 42.97 3.11
2719 7459 2.836981 AGAGTTGCTCATAGCTGTCCTT 59.163 45.455 0.00 0.00 42.97 3.36
2720 7460 2.168106 CAGAGTTGCTCATAGCTGTCCT 59.832 50.000 0.00 0.00 42.97 3.85
2721 7461 2.548875 CAGAGTTGCTCATAGCTGTCC 58.451 52.381 0.00 0.00 42.97 4.02
2722 7462 2.167281 TCCAGAGTTGCTCATAGCTGTC 59.833 50.000 0.00 0.00 42.97 3.51
2723 7463 2.093764 GTCCAGAGTTGCTCATAGCTGT 60.094 50.000 0.00 0.00 42.97 4.40
2724 7464 2.168106 AGTCCAGAGTTGCTCATAGCTG 59.832 50.000 0.00 0.00 42.97 4.24
2727 7467 4.462508 TGAAGTCCAGAGTTGCTCATAG 57.537 45.455 0.00 0.00 32.06 2.23
2728 7468 5.426689 AATGAAGTCCAGAGTTGCTCATA 57.573 39.130 0.00 0.00 32.06 2.15
2729 7469 3.996921 ATGAAGTCCAGAGTTGCTCAT 57.003 42.857 0.00 0.00 32.06 2.90
2731 7471 6.456181 CGATAAAATGAAGTCCAGAGTTGCTC 60.456 42.308 0.00 0.00 0.00 4.26
2732 7472 5.352569 CGATAAAATGAAGTCCAGAGTTGCT 59.647 40.000 0.00 0.00 0.00 3.91
2733 7473 5.351465 TCGATAAAATGAAGTCCAGAGTTGC 59.649 40.000 0.00 0.00 0.00 4.17
2734 7474 6.968131 TCGATAAAATGAAGTCCAGAGTTG 57.032 37.500 0.00 0.00 0.00 3.16
2735 7475 9.838339 AATATCGATAAAATGAAGTCCAGAGTT 57.162 29.630 9.61 0.00 0.00 3.01
3280 8024 6.236017 TGCCTAAGTTCACAAGTTTTATCG 57.764 37.500 0.00 0.00 0.00 2.92
3386 8130 5.047872 TGCATGCAATTGTGATAGTTCTTGT 60.048 36.000 20.30 0.00 0.00 3.16
3446 8190 7.930865 TGTCCCAGGAAACAAATGAAAATTAAG 59.069 33.333 0.00 0.00 0.00 1.85
3579 8323 0.468226 ACACTGCCAGGAACGAAAGA 59.532 50.000 0.00 0.00 0.00 2.52
3584 8328 2.639286 GCAACACTGCCAGGAACG 59.361 61.111 0.00 0.00 43.26 3.95
3611 8355 2.156098 TCAACGTTTGGGTATGCCTTC 58.844 47.619 0.00 0.00 34.45 3.46
3823 8641 9.621629 ATGATTCAAAAATTACATGGCATCAAT 57.378 25.926 0.00 0.00 0.00 2.57
3825 8643 9.451002 AAATGATTCAAAAATTACATGGCATCA 57.549 25.926 0.00 0.00 0.00 3.07
4172 8997 1.879575 ATAGGGGCTGAGTACTTGCA 58.120 50.000 18.94 4.49 0.00 4.08
4218 9043 7.282224 ACACTTCAACACACTCAAGCTTAATTA 59.718 33.333 0.00 0.00 0.00 1.40
4256 9081 1.202428 CCGAACTGAAGGTAGCTAGGC 60.202 57.143 0.00 0.00 0.00 3.93
4330 9156 4.068599 AGCCAAGACTTAAACTCAAGAGC 58.931 43.478 0.00 0.00 0.00 4.09
4331 9157 6.625873 AAAGCCAAGACTTAAACTCAAGAG 57.374 37.500 0.00 0.00 0.00 2.85
4341 9167 7.096551 GGATAAATTGCAAAAGCCAAGACTTA 58.903 34.615 1.71 0.00 0.00 2.24
4372 9198 0.980231 ACAAAGGGGGCAACAGCAAA 60.980 50.000 0.00 0.00 39.74 3.68
4379 9205 1.706995 TACGTGGACAAAGGGGGCAA 61.707 55.000 0.00 0.00 0.00 4.52
4413 9262 4.023622 CACGTGGATAGACTCAGAGGTATG 60.024 50.000 7.95 0.00 0.00 2.39
4430 9279 2.604174 GCGGGAAGTCAACACGTGG 61.604 63.158 21.57 2.57 36.49 4.94
4524 9373 1.167851 GCTTCATGCACTAGCCAACA 58.832 50.000 5.46 0.00 42.31 3.33
4561 9410 5.581085 CCAGGGTCAAATAAGAGAAACTACG 59.419 44.000 0.00 0.00 0.00 3.51
4621 9470 8.424274 ACCAATGATCAAAACAAGAGAAAAAC 57.576 30.769 0.00 0.00 0.00 2.43
4625 9474 8.352201 CAGTAACCAATGATCAAAACAAGAGAA 58.648 33.333 0.00 0.00 0.00 2.87
4950 9799 6.994421 ACCAACAGAAATTAAGGAATGGTT 57.006 33.333 0.00 0.00 35.20 3.67
5014 9863 3.007506 TCGGACCTCTCAGCAATTAACAA 59.992 43.478 0.00 0.00 0.00 2.83
5119 9968 5.473162 TGACAAATCGATGACCATGAAAAGT 59.527 36.000 0.00 0.00 0.00 2.66
5182 10032 4.901197 TGATTGGTAAAGGTCAGCACTA 57.099 40.909 0.00 0.00 0.00 2.74
5189 10039 5.185828 AGGAAGCAAATGATTGGTAAAGGTC 59.814 40.000 0.00 0.00 46.06 3.85
5478 10484 7.902920 AATTATTTAGCATCCATGGTTCAGT 57.097 32.000 12.58 0.00 39.52 3.41
5528 10534 4.898320 TCTCAGAAGTTAAGCAAGCATGA 58.102 39.130 0.00 0.00 0.00 3.07
5607 10623 1.065031 GCAACGGCACTTACGCATTG 61.065 55.000 0.00 0.00 40.72 2.82
5825 10841 9.868160 CCCTCCATTCCTAAATATAAGTCTTTT 57.132 33.333 0.00 0.00 0.00 2.27
5829 10845 8.208575 ACTCCCTCCATTCCTAAATATAAGTC 57.791 38.462 0.00 0.00 0.00 3.01
5834 10850 8.997301 AAGATACTCCCTCCATTCCTAAATAT 57.003 34.615 0.00 0.00 0.00 1.28
5845 10861 5.671463 AGTCTATGAAGATACTCCCTCCA 57.329 43.478 0.00 0.00 33.30 3.86
5863 10879 0.178912 ACCGAACACCCCCTAAGTCT 60.179 55.000 0.00 0.00 0.00 3.24
5864 10880 0.689055 AACCGAACACCCCCTAAGTC 59.311 55.000 0.00 0.00 0.00 3.01
5865 10881 0.399075 CAACCGAACACCCCCTAAGT 59.601 55.000 0.00 0.00 0.00 2.24
5866 10882 0.958876 GCAACCGAACACCCCCTAAG 60.959 60.000 0.00 0.00 0.00 2.18
5867 10883 1.073548 GCAACCGAACACCCCCTAA 59.926 57.895 0.00 0.00 0.00 2.69
5868 10884 2.148052 TGCAACCGAACACCCCCTA 61.148 57.895 0.00 0.00 0.00 3.53
5869 10885 3.494254 TGCAACCGAACACCCCCT 61.494 61.111 0.00 0.00 0.00 4.79
5870 10886 3.292159 GTGCAACCGAACACCCCC 61.292 66.667 0.00 0.00 0.00 5.40
5871 10887 3.656045 CGTGCAACCGAACACCCC 61.656 66.667 0.00 0.00 33.09 4.95
5872 10888 3.656045 CCGTGCAACCGAACACCC 61.656 66.667 0.00 0.00 33.09 4.61
5873 10889 3.656045 CCCGTGCAACCGAACACC 61.656 66.667 0.00 0.00 33.09 4.16
5874 10890 2.589442 TCCCGTGCAACCGAACAC 60.589 61.111 0.00 0.00 0.00 3.32
5875 10891 1.746322 TAGTCCCGTGCAACCGAACA 61.746 55.000 0.00 0.00 0.00 3.18
5876 10892 0.390735 ATAGTCCCGTGCAACCGAAC 60.391 55.000 0.00 0.00 0.00 3.95
5877 10893 0.390603 CATAGTCCCGTGCAACCGAA 60.391 55.000 0.00 0.00 0.00 4.30
5878 10894 1.216977 CATAGTCCCGTGCAACCGA 59.783 57.895 0.00 0.00 0.00 4.69
5879 10895 0.390603 TTCATAGTCCCGTGCAACCG 60.391 55.000 0.00 0.00 0.00 4.44
5880 10896 1.084289 GTTCATAGTCCCGTGCAACC 58.916 55.000 0.00 0.00 0.00 3.77
5881 10897 2.094762 AGTTCATAGTCCCGTGCAAC 57.905 50.000 0.00 0.00 0.00 4.17
5882 10898 2.851263 AAGTTCATAGTCCCGTGCAA 57.149 45.000 0.00 0.00 0.00 4.08
5883 10899 2.851263 AAAGTTCATAGTCCCGTGCA 57.149 45.000 0.00 0.00 0.00 4.57
5928 10944 8.208575 AGAAAAAGACTCTACTGAAGGGTATT 57.791 34.615 0.00 0.00 42.00 1.89
5929 10945 7.800300 AGAAAAAGACTCTACTGAAGGGTAT 57.200 36.000 0.00 0.00 39.82 2.73
5930 10946 8.716674 TTAGAAAAAGACTCTACTGAAGGGTA 57.283 34.615 0.00 0.00 39.82 3.69
5931 10947 7.613551 TTAGAAAAAGACTCTACTGAAGGGT 57.386 36.000 0.00 0.00 43.68 4.34
5932 10948 7.766738 GGATTAGAAAAAGACTCTACTGAAGGG 59.233 40.741 0.00 0.00 0.00 3.95
5933 10949 7.766738 GGGATTAGAAAAAGACTCTACTGAAGG 59.233 40.741 0.00 0.00 0.00 3.46
5934 10950 8.536175 AGGGATTAGAAAAAGACTCTACTGAAG 58.464 37.037 0.00 0.00 0.00 3.02
5935 10951 8.437274 AGGGATTAGAAAAAGACTCTACTGAA 57.563 34.615 0.00 0.00 0.00 3.02
5936 10952 9.543231 TTAGGGATTAGAAAAAGACTCTACTGA 57.457 33.333 0.00 0.00 0.00 3.41
5948 10964 9.524496 GGGACTTTTACTTTAGGGATTAGAAAA 57.476 33.333 0.00 0.00 0.00 2.29
5949 10965 8.897692 AGGGACTTTTACTTTAGGGATTAGAAA 58.102 33.333 0.00 0.00 27.25 2.52
5950 10966 8.458951 AGGGACTTTTACTTTAGGGATTAGAA 57.541 34.615 0.00 0.00 27.25 2.10
5951 10967 7.126879 GGAGGGACTTTTACTTTAGGGATTAGA 59.873 40.741 0.00 0.00 41.55 2.10
5952 10968 7.127493 AGGAGGGACTTTTACTTTAGGGATTAG 59.873 40.741 0.00 0.00 41.55 1.73
5953 10969 6.970041 AGGAGGGACTTTTACTTTAGGGATTA 59.030 38.462 0.00 0.00 41.55 1.75
5954 10970 5.796399 AGGAGGGACTTTTACTTTAGGGATT 59.204 40.000 0.00 0.00 41.55 3.01
5955 10971 5.191921 CAGGAGGGACTTTTACTTTAGGGAT 59.808 44.000 0.00 0.00 41.55 3.85
5956 10972 4.534897 CAGGAGGGACTTTTACTTTAGGGA 59.465 45.833 0.00 0.00 41.55 4.20
5957 10973 4.288887 ACAGGAGGGACTTTTACTTTAGGG 59.711 45.833 0.00 0.00 41.55 3.53
5958 10974 5.500546 ACAGGAGGGACTTTTACTTTAGG 57.499 43.478 0.00 0.00 41.55 2.69
5959 10975 6.996282 TCAAACAGGAGGGACTTTTACTTTAG 59.004 38.462 0.00 0.00 41.55 1.85
5960 10976 6.902408 TCAAACAGGAGGGACTTTTACTTTA 58.098 36.000 0.00 0.00 41.55 1.85
5961 10977 5.762279 TCAAACAGGAGGGACTTTTACTTT 58.238 37.500 0.00 0.00 41.55 2.66
5962 10978 5.382664 TCAAACAGGAGGGACTTTTACTT 57.617 39.130 0.00 0.00 41.55 2.24
5963 10979 5.584551 ATCAAACAGGAGGGACTTTTACT 57.415 39.130 0.00 0.00 41.55 2.24
5964 10980 6.713450 TGTAATCAAACAGGAGGGACTTTTAC 59.287 38.462 0.00 0.00 41.55 2.01
5965 10981 6.843752 TGTAATCAAACAGGAGGGACTTTTA 58.156 36.000 0.00 0.00 41.55 1.52
5966 10982 5.701224 TGTAATCAAACAGGAGGGACTTTT 58.299 37.500 0.00 0.00 41.55 2.27
5967 10983 5.319043 TGTAATCAAACAGGAGGGACTTT 57.681 39.130 0.00 0.00 41.55 2.66
5968 10984 4.993705 TGTAATCAAACAGGAGGGACTT 57.006 40.909 0.00 0.00 41.55 3.01
5969 10985 5.131142 CCTATGTAATCAAACAGGAGGGACT 59.869 44.000 0.00 0.00 34.77 3.85
5970 10986 5.368989 CCTATGTAATCAAACAGGAGGGAC 58.631 45.833 0.00 0.00 34.77 4.46
5971 10987 5.630415 CCTATGTAATCAAACAGGAGGGA 57.370 43.478 0.00 0.00 34.77 4.20
5972 10988 4.718961 CCCTATGTAATCAAACAGGAGGG 58.281 47.826 10.66 10.66 44.22 4.30
5973 10989 5.630415 TCCCTATGTAATCAAACAGGAGG 57.370 43.478 0.00 0.00 36.69 4.30
5974 10990 9.627123 TTTAATCCCTATGTAATCAAACAGGAG 57.373 33.333 0.00 0.00 31.70 3.69
5975 10991 9.983024 TTTTAATCCCTATGTAATCAAACAGGA 57.017 29.630 0.00 0.00 31.70 3.86
5981 10997 9.847224 GGTCTCTTTTAATCCCTATGTAATCAA 57.153 33.333 0.00 0.00 0.00 2.57
5982 10998 9.225682 AGGTCTCTTTTAATCCCTATGTAATCA 57.774 33.333 0.00 0.00 0.00 2.57
5999 11015 8.840833 GAGACAAGATTAGAAAAGGTCTCTTT 57.159 34.615 10.66 0.00 43.81 2.52
6002 11018 7.382898 ACAGAGACAAGATTAGAAAAGGTCTC 58.617 38.462 10.09 10.09 46.16 3.36
6003 11019 7.309770 ACAGAGACAAGATTAGAAAAGGTCT 57.690 36.000 0.00 0.00 40.71 3.85
6004 11020 8.927721 GTTACAGAGACAAGATTAGAAAAGGTC 58.072 37.037 0.00 0.00 0.00 3.85
6005 11021 7.878644 GGTTACAGAGACAAGATTAGAAAAGGT 59.121 37.037 0.00 0.00 0.00 3.50
6006 11022 7.878127 TGGTTACAGAGACAAGATTAGAAAAGG 59.122 37.037 0.00 0.00 0.00 3.11
6007 11023 8.833231 TGGTTACAGAGACAAGATTAGAAAAG 57.167 34.615 0.00 0.00 0.00 2.27
6008 11024 9.621629 TTTGGTTACAGAGACAAGATTAGAAAA 57.378 29.630 0.00 0.00 0.00 2.29
6009 11025 9.052759 GTTTGGTTACAGAGACAAGATTAGAAA 57.947 33.333 0.00 0.00 0.00 2.52
6010 11026 8.208224 TGTTTGGTTACAGAGACAAGATTAGAA 58.792 33.333 0.00 0.00 0.00 2.10
6011 11027 7.732025 TGTTTGGTTACAGAGACAAGATTAGA 58.268 34.615 0.00 0.00 0.00 2.10
6012 11028 7.118390 CCTGTTTGGTTACAGAGACAAGATTAG 59.882 40.741 5.39 0.00 46.72 1.73
6013 11029 6.934645 CCTGTTTGGTTACAGAGACAAGATTA 59.065 38.462 5.39 0.00 46.72 1.75
6014 11030 5.765182 CCTGTTTGGTTACAGAGACAAGATT 59.235 40.000 5.39 0.00 46.72 2.40
6015 11031 5.308825 CCTGTTTGGTTACAGAGACAAGAT 58.691 41.667 5.39 0.00 46.72 2.40
6016 11032 4.444306 CCCTGTTTGGTTACAGAGACAAGA 60.444 45.833 5.39 0.00 46.72 3.02
6017 11033 3.815401 CCCTGTTTGGTTACAGAGACAAG 59.185 47.826 5.39 0.00 46.72 3.16
6018 11034 3.815809 CCCTGTTTGGTTACAGAGACAA 58.184 45.455 5.39 0.00 46.72 3.18
6019 11035 2.486548 GCCCTGTTTGGTTACAGAGACA 60.487 50.000 5.39 0.00 46.72 3.41
6020 11036 2.152016 GCCCTGTTTGGTTACAGAGAC 58.848 52.381 5.39 0.00 46.72 3.36
6021 11037 1.073284 GGCCCTGTTTGGTTACAGAGA 59.927 52.381 5.39 0.00 46.72 3.10
6022 11038 1.073923 AGGCCCTGTTTGGTTACAGAG 59.926 52.381 0.00 0.00 46.72 3.35
6023 11039 1.145571 AGGCCCTGTTTGGTTACAGA 58.854 50.000 0.00 0.00 46.72 3.41
6024 11040 1.995376 AAGGCCCTGTTTGGTTACAG 58.005 50.000 0.00 0.00 44.07 2.74
6025 11041 3.818295 ATAAGGCCCTGTTTGGTTACA 57.182 42.857 0.00 0.00 0.00 2.41


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.